User:Alexander.lex/caleydo

Caleydo is an open source bioinformatics software platform for visualizing and data analysis of heterogeneous biomolecular data. It allows users to analyse tabular data sources such as gene expression, mutation or copy number data as well as graph data in the form of biological pathways.

History
Caleydo was created in 2008 using sources of GeneView at the Institute of Computer Graphics at the Graz University of Technology in Austria. Caleydo is now developed by multiple academic institutions including [Harvard University] and [Johannes Kepler University Linz]. Caleydo was made available free for academic use in October 2008 (v1.0); the second release (v1.1) was in March, 2009; the third (v1.2) in May 2009. The final release of the 1.x series, v1.3 was released in February 2010. Caleydo was made open source with the release of Version 2.0, which included StratomeX, a visualization technique for cancer subtype analysis. The latest major release of Caleydo is version 3 (released in July 2013) which introduces novel methods for visualizing pathways and experimental data and overhauls the cancer subtype visualization to include computational tools.

Development
Caledyo is developed jointly by partners from the Graz University of Technology, Johannes Kepler University Linz and Harvard University. Development is funded through various public research grants. Caleydo is based on RCP and uses OpenGL for high-performance rendering.

Features
Input

Caleydo can read comma-separated text files as input for matrices of various formats and understands a wide range of gene identifiers. It comes pre-packaged with pathway databases.

Visualization

Analysis